Hi I am new to RNA seq analysis. I am trying to run bowtie2 in command line but failed. can somebody help with the code
qsub -l h_data=4G,time=2:00:00 -cwd -b y ‘module load bowtie2; bowtie2 -p 4 -x Bowtie2Index -1N704.fastq -S bowtie.N704’
also I would like to know if I can get a separate file for unaligned reads.